Hello there, 

This is how I proceed in such cases.  Mail the parents' paper tax return and provide the reason code on line 4 of the 8948 form (Preparer Explanation for Not Filing Electronically).  Once the IRS processes this return, they will be aware of the issue and confirm that the son filed a 1040X (as a dependent).  This also provides a paper trail confirming the tax return was timely filed, but rejected.  Since it is a paper tax return and there are issues to be clarified, this will take about 6 months for any refund.  Of course, this has generated additional time and effort on your part; charge accordingly or create goodwill by charging a nominal fee if any.  Gracias.